This is a test version of Biostars. For the public version, visit https://www.biostars.org.
download WGS from dbGAP authorized with prefetch tools

Hi

I would like to download some WGS from dbgap with prefetch.2.9.1. But I get the below message:

2018-08-27T23:17:32 prefetch.2.9.1 warn: Maximum file size download limit is 20GB 2018-08-27T23:17:32 prefetch.2.9.1: 7) 'SRRXXXX' (316GB) is larger than maximum allowed: skipped

How can I fix this? should I use other tools?

Thanks Sara

wgs dbgap
• 5,153 views • link
updated by ATpoint ATpoint • written by jonessara770 jonessara770

1 answer

Prefetch has a default limitation to only allow downloads of files no more than 20GB in size. I am guessing that this is a relict from times when disk space was actually a concern. Increase that limit using this parameter:

-X | --max-size <size>             maximum file size to download in KB 
                                   (exclusive). Default: 20G 


./prefetch -X 9999999999999 SRRXXX

When these things happen, typically one finds the answer when running the tools without any parameters or with -h to display the help section ;-)

• 1 views • link
written by ATpoint ATpoint

Log in to answer this question.

More posts like this